Support package data

[kamilzyla]

It seems that box doesn't handle datasets exported from packages:

> box::use(datasets[mtcars])
Error in attach_list(spec, names(mod_exports)) : 
  Name “mtcars” not exported by datasets
> datasets::mtcars # Works fine

Perhaps the problem is lazy loading of data? This happens on other packages as well, e.g. box::use(zipcodeR[zip_code_db]).

[klmr]

Yep, it’s because of lazy loading, which works completely different from regular exports, and is currently not supported.

It’s low priority but there should be a ticket to track it, so this is now it.

[klmr]

Implemented now. To preview before the next release, install the dev build of ‘box’ via

install.packages('box', repos = 'https://klmr.r-universe.dev')

[nvelden]

Hello,

I'm encountering an issue where I'm able to load data in a Shiny app, but unable to do the same within a Shiny module. Here's a minimal working example:

My main app:

# Load necessary libraries
library(shiny)
library(shinydashboard)
library(SBGNview)

box::use(./table_module[table_module_UI, table_module])

# Define UI for application
ui <- dashboardPage(
  dashboardHeader(title = "Displaying First 10 Rows of Pathways.info"),
  dashboardSidebar(),
  dashboardBody(
    box(
      title = "Data", 
      status = "primary", 
      solidHeader = TRUE, 
      width = 12,
      table_module_UI("data_table")
    )
  )
)

# Define server logic
server <- function(input, output, session) {
  
  data("pathways.info", package = "SBGNview")
  
  # Call the table_module
  callModule(table_module, "data_table", pathways.info[1:10,])
}

# Run the application 
shinyApp(ui = ui, server = server)

And my table_module.R:

box::use(
  shiny[NS],
  SBGNview[...],
  DT[renderDT, DTOutput],
  utils[data])

# Define the UI for the table module
table_module_UI <- function(id) {
  ns <- NS(id)
  DTOutput(ns("table"))
}

# Define the server for the table module
table_module <- function(input, output, session, data) {
  output$table <- DT::renderDT({
    # Load pathways.info data
    data
  })
}

In the main app, I'm able to load the pathways.info dataset from the SBGNview package. However, when I try to load the data in the table_module, the data does not load.

# Load necessary libraries
library(shiny)
library(shinydashboard)
library(SBGNview)

box::use(./table_module[table_module_UI, table_module])

# Define UI for application
ui <- dashboardPage(
  dashboardHeader(title = "Displaying First 10 Rows of Pathways.info"),
  dashboardSidebar(),
  dashboardBody(
    box(
      title = "Data", 
      status = "primary", 
      solidHeader = TRUE, 
      width = 12,
      table_module_UI("data_table")
    )
  )
)

# Define server logic
server <- function(input, output, session) {
  
  # Call the table_module
  callModule(table_module, "data_table")
}

# Run the application 
shinyApp(ui = ui, server = server)

# Load necessary libraries
box::use(
  shiny[NS],
  SBGNview[...],
  DT[renderDT, DTOutput],
  utils[data])

# Define the UI for the table module
table_module_UI <- function(id) {
  ns <- NS(id)
  DTOutput(ns("table"))
}

# Define the server for the table module
table_module <- function(input, output, session) {
  output$table <- DT::renderDT({
    
    # Load pathways.info data
    data("pathways.info", package = "SBGNview")
    
    # Extract first 10 rows
    pathways_data <- pathways.info[1:10,]
    
    output$table <- DT::renderDT({
      pathways_data
    })
  })
}

Warning: Error in exprFunc: object 'pathways.info' not found

Any ideas as to why this is happening and how I could fix it?

[klmr]

I can’t reproduce this because I can’t install ‘SBGNview’ (in particular, its transitive dependency ‘Rgraphviz’ fails to compile).

But there are a few issues with the second code you’ve posted that need to be fixed:

1. data() will load the data independently of box::use() (in fact, it should work even if you didn’t load the package via box::use()).
2. But data() loads the data in the global environment. This is a deficiency in data(), but it’s unrelated to ‘box’ (in fact, you get the same effect without using ‘box’!). So to load the data inside a Shiny module you’d need to use data("pathways.info", package = "SBGNview", envir = environment()).
3. You have an error in table_module: you have output$table <- DT::renderDT() twice, one nested inside the other. Remove the outer invocation.

To summarise, the issue is three-fold:

1. ‘SBGNview’ uses LazyData: false, which means that data is not loaded when the package is loaded. It needs to be explicitly loaded via data().
2. But data() loads data into the global namespace by default, unless envir = environment() is specified.
3. And Shiny modules are intentionally isolated from the global environment, so they don’t see objects that are loaded into the global environment.

This is unrelated to ‘box’, you’d have the same issue if you tried loading the package via library() instead of box::use() (and in fact neither of these expressions loads the package data).

[nvelden]

Thanks a lot! Loading the data using data("pathways.info", package = "SBGNview", envir = environment()) in the Shiny box module solved my issue.